New approach to an old problem: Incorporating signal from gap-rich regions of ITS and rDNA large subunit into phylogenetic analyses to resolve the<i>Peltigera canina</i>species complex

The Peltigera canina species complex consists of foliose lichenized bitunicate ascohymenial discomycetes forming section Peltigera within the genus Peltigera (Lecanoromycetes, lichen-forming Ascomycetes). To test the circumscription of highly polymorphic species and to resolve relationships among putative members of the P. canina complex, part of the nuclear ribosomal DNA large subunit (LSU rDNA) and the entire internal-transcribed spacer (ITS rDNA) were sequenced for 84 individuals representing 33 putative Peltigera taxa. Seventeen of the 25 taxa from the P. canina complex are well established and widely accepted. The remaining eight taxa have been proposed recently but are undescribed. A hypervariable region in ITS1 (ITS1-HR, sites 111-237 in our alignment) showed remarkable variation in length, especially in the P. canina complex, ranging from 8 to 126 bp, and contained several microsatellites. We describe here an alignment-free method to code such large gap-rich hypervariable regions for phylogenetic analyses. Variation among ITS1-HR sequences greatly contributed to species delimitation and species identification and can be a major asset to future population studies for specific species within section Peltigera. Sequences of ITS1-HR alone were sufficient to identify all existing species of Peltigera from the P. canina species complex and related sections Retifoveatae and Horizontales included in this study. However, only when INAASE (for short ambiguously aligned regions) and ITS1-HR coded characters were added to the combined analysis of nonambiguous LSU and ITS sites was it possible to reach the level of phylogenetic resolution and support necessary to disentangle the P. canina complex. We report here complete concordance between phylogenetically based and morphologically based species delimitation for 15 of the 17 species from the P. canina complex (P. canina, P. cinnamomea, P. degenii, P. evansiana, P. frigida, P. kristinssonii, P. laciniata, P. lambinonii, P. lepidophora, P. membranacea, P. monticola, P. ponojensis, P. praetextata, P. rufescens and P. ulcerata). Four of the eight newly proposed but undescribed taxa most likely represent new species (P. "fuscopraetextata", P. "neocanina", P. "neorufescens" and P. "scotteri") within the P. canina complex. We found that morphologically and chemically distinct P. didactyla s. str. and P. didactyla var. extenuata form two non-sister monophyletic entities, therefore the latter taxon should be recognized at the species level (P. extenuata). The North American and European populations of the morphologically uniform P. degenii might represent two sibling species because they were found to be genetically distinct and monophyletic. Two major monophyletic groups within the P. canina complex (CICADE = CInnamomea + CAnina + DEgenii group and PORUDI = POnojensis + RUfescens + DIdactyla group) seem to be correlated with different humidity preferences. Although some authors previously have suggested interspecies recombination within the P. canina complex, we did not find statistically significant evidence for this phenomenon based on LSU and ITS sequences.